[English] 日本語
Yorodumi
- PDB-7xlz: Structure of siderophore-interacting protein from Vibrio anguillarum -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xlz
TitleStructure of siderophore-interacting protein from Vibrio anguillarum
ComponentsSiderophore-interacting protein
KeywordsOXIDOREDUCTASE / siderophore-interacting protein / iron release / Vibrio anguillarum
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
Siderophore-interacting protein / Siderophore-interacting protein, C-terminal domain / FAD-binding 9, siderophore-interacting / Siderophore-interacting protein / Siderophore-interacting FAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Siderophore-interacting protein
Similarity search - Component
Biological speciesVibrio anguillarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å
AuthorsMa, Q. / Liu, C. / Han, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of siderophore-interacting protein from Vibrio anguillarum
Authors: Ma, Q. / Liu, C. / Han, Y.
History
DepositionApr 23, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Siderophore-interacting protein
B: Siderophore-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6754
Polymers60,1032
Non-polymers1,5712
Water10,935607
1
A: Siderophore-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8372
Polymers30,0521
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-8 kcal/mol
Surface area12060 Å2
MethodPISA
2
B: Siderophore-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8372
Polymers30,0521
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-8 kcal/mol
Surface area12030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.622, 58.466, 70.650
Angle α, β, γ (deg.)90.000, 114.180, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 10:25 or (resid 26 and (name...
21(chain B and ((resid 10 and (name N or name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERSERSER(chain A and (resseq 10:25 or (resid 26 and (name...AA10 - 2513 - 28
12LEULEULEULEU(chain A and (resseq 10:25 or (resid 26 and (name...AA2629
13SERSERFADFAD(chain A and (resseq 10:25 or (resid 26 and (name...AA - C10 - 30113
14SERSERFADFAD(chain A and (resseq 10:25 or (resid 26 and (name...AA - C10 - 30113
15SERSERFADFAD(chain A and (resseq 10:25 or (resid 26 and (name...AA - C10 - 30113
16SERSERFADFAD(chain A and (resseq 10:25 or (resid 26 and (name...AA - C10 - 30113
17SERSERFADFAD(chain A and (resseq 10:25 or (resid 26 and (name...AA - C10 - 30113
18SERSERFADFAD(chain A and (resseq 10:25 or (resid 26 and (name...AA - C10 - 30113
19SERSERFADFAD(chain A and (resseq 10:25 or (resid 26 and (name...AA - C10 - 30113
110SERSERFADFAD(chain A and (resseq 10:25 or (resid 26 and (name...AA - C10 - 30113
111SERSERFADFAD(chain A and (resseq 10:25 or (resid 26 and (name...AA - C10 - 30113
112SERSERFADFAD(chain A and (resseq 10:25 or (resid 26 and (name...AA - C10 - 30113
113SERSERFADFAD(chain A and (resseq 10:25 or (resid 26 and (name...AA - C10 - 30113
114SERSERFADFAD(chain A and (resseq 10:25 or (resid 26 and (name...AA - C10 - 30113
115SERSERFADFAD(chain A and (resseq 10:25 or (resid 26 and (name...AA - C10 - 30113
116SERSERFADFAD(chain A and (resseq 10:25 or (resid 26 and (name...AA - C10 - 30113
21SERSERSERSER(chain B and ((resid 10 and (name N or name...BB1013
22ARGARGFADFAD(chain B and ((resid 10 and (name N or name...BB - D9 - 30112
23ARGARGFADFAD(chain B and ((resid 10 and (name N or name...BB - D9 - 30112
24ARGARGFADFAD(chain B and ((resid 10 and (name N or name...BB - D9 - 30112
25ARGARGFADFAD(chain B and ((resid 10 and (name N or name...BB - D9 - 30112
26ARGARGFADFAD(chain B and ((resid 10 and (name N or name...BB - D9 - 30112
27ARGARGFADFAD(chain B and ((resid 10 and (name N or name...BB - D9 - 30112
28ARGARGFADFAD(chain B and ((resid 10 and (name N or name...BB - D9 - 30112
29ARGARGFADFAD(chain B and ((resid 10 and (name N or name...BB - D9 - 30112
210ARGARGFADFAD(chain B and ((resid 10 and (name N or name...BB - D9 - 30112

-
Components

#1: Protein Siderophore-interacting protein / vaSIP


Mass: 30051.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio anguillarum (strain ATCC 68554 / 775) (bacteria)
Strain: ATCC 68554 / 775 / Gene: VAA_01637 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: F7YRY1
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 607 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: The crystal of VaSIP was grown in the drop containing 1.4 ul protein solution (60 mg/ml in 10 mM Hepes, 150 mM NaCl, pH 7.5, 1 mM DTT) and 1.4 ul reservoir solution (0.1 M KBr, 30% (W/V) mPEG 2000).

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.19→58.951 Å / Num. obs: 147256 / % possible obs: 95.8 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rpim(I) all: 0.021 / Rrim(I) all: 0.055 / Rsym value: 0.051 / Net I/σ(I): 20.2
Reflection shellResolution: 1.19→1.194 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1171 / CC1/2: 0.885 / Rpim(I) all: 0.21 / Rrim(I) all: 0.528 / Rsym value: 0.482 / % possible all: 74.6

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
XDSJan 10, 2022, built on 20220220data reduction
Aimlessversion 0.5.29data scaling
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2gpj

2gpj


Resolution: 1.19→58.951 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1615 7417 5.04 %
Rwork0.1378 139797 -
obs0.139 147214 95.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 46.2 Å2 / Biso mean: 14.8159 Å2 / Biso min: 5.65 Å2
Refinement stepCycle: final / Resolution: 1.19→58.951 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3877 0 106 607 4590
Biso mean--7.76 25.05 -
Num. residues----487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084132
X-RAY DIFFRACTIONf_angle_d1.0325627
X-RAY DIFFRACTIONf_chiral_restr0.081611
X-RAY DIFFRACTIONf_plane_restr0.007794
X-RAY DIFFRACTIONf_dihedral_angle_d18.3941577
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2331X-RAY DIFFRACTION6.925TORSIONAL
12B2331X-RAY DIFFRACTION6.925TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.19-1.20320.20181760.1757387880
1.2032-1.21740.19372300.1695438190
1.2174-1.23220.19392490.1838453095
1.2322-1.24780.19852230.1537464195
1.2478-1.26430.2382310.2048462795
1.2643-1.28160.18552210.1604461296
1.2816-1.29990.21332340.1692461794
1.2999-1.31930.17532550.1428462996
1.3193-1.33990.16382810.1318460195
1.3399-1.36190.18642570.1414454894
1.3619-1.38540.20152310.1538466396
1.3854-1.41060.15052550.1211466597
1.4106-1.43770.14772610.1296466897
1.4377-1.4670.15612340.1341472696
1.467-1.4990.17742460.1306467796
1.499-1.53380.18612490.1342468297
1.5338-1.57220.13312260.1091453993
1.5722-1.61470.15432380.1099468996
1.6147-1.66220.13622410.1101473698
1.6622-1.71590.1392690.1136474298
1.7159-1.77720.1482670.116475498
1.7772-1.84840.14422340.1266481698
1.8484-1.93250.1672540.1352468397
1.9325-2.03440.15222390.1277469296
2.0344-2.16180.16012330.1329482198
2.1618-2.32880.14252600.1357481599
2.3288-2.56310.15332600.1346486099
2.5631-2.9340.16882900.1465473197
2.934-3.69640.15613000.14434858100
3.6964-58.9510.16622730.1459491698

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more